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Yorodumi- PDB-2w55: Crystal Structure of Xanthine Dehydrogenase (E232Q variant) from ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2w55 | ||||||
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Title | Crystal Structure of Xanthine Dehydrogenase (E232Q variant) from Rhodobacter capsulatus in Complex with Hypoxanthine | ||||||
Components | (XANTHINE DEHYDROGENASE) x 2 | ||||||
Keywords | OXIDOREDUCTASE / XDH / GOUT / IRON / XANTHINE / IRON-SULFUR / MOLYBDENUM COFACTOR / HYPOXANTHINE / METAL-BINDING | ||||||
Function / homology | Function and homology information 1.1.1.204 / xanthine dehydrogenase activity / molybdenum ion binding / FAD binding / 2 iron, 2 sulfur cluster binding / oxidoreductase activity / iron ion binding Similarity search - Function | ||||||
Biological species | RHODOBACTER CAPSULATUS (bacteria) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.4 Å | ||||||
Authors | Doebbler, J.A. / Truglio, J.J. / Leimkuhler, S. / Kisker, C. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2009 Title: Mechanism of Substrate and Inhibitor Binding of Rhodobacter Capsulatus Xanthine Dehydrogenase. Authors: Dietzel, U. / Kuper, J. / Doebbler, J.A. / Schulte, A. / Truglio, J.J. / Leimkuhler, S. / Kisker, C. | ||||||
History |
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Remark 700 | SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED. |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2w55.cif.gz | 876.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2w55.ent.gz | 706 KB | Display | PDB format |
PDBx/mmJSON format | 2w55.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w5/2w55 ftp://data.pdbj.org/pub/pdb/validation_reports/w5/2w55 | HTTPS FTP |
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-Related structure data
Related structure data | 2w3rC 2w3sC 2w54C 1jroS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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4 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1
NCS ensembles :
NCS oper:
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-Components
-Protein , 2 types, 8 molecules ACEGBDFH
#1: Protein | Mass: 49420.508 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) RHODOBACTER CAPSULATUS (bacteria) / Plasmid: PSL207 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TP1000 / References: UniProt: O54050, 1.1.1.204 #2: Protein | Mass: 82977.047 Da / Num. of mol.: 4 / Mutation: YES Source method: isolated from a genetically manipulated source Source: (gene. exp.) RHODOBACTER CAPSULATUS (bacteria) / Plasmid: PSL207 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): TP1000 / References: UniProt: O54051, 1.1.1.204 |
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-Non-polymers , 6 types, 67 molecules
#3: Chemical | ChemComp-FES / #4: Chemical | ChemComp-FAD / #5: Chemical | ChemComp-XAX / {[( #6: Chemical | ChemComp-BA / #7: Chemical | ChemComp-HPA / #8: Water | ChemComp-HOH / | |
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-Details
Compound details | ENGINEERED RESIDUE IN CHAIN B, GLU 232 TO GLN ENGINEERED RESIDUE IN CHAIN D, GLU 232 TO GLN ...ENGINEERED |
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Sequence details | E232Q VARIANT |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.35 Å3/Da / Density % sol: 63.25 % / Description: NONE |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 8.3 Details: 100 MM TRIS PH 8.3, 6-8 % PEG 8000, 6-8 MM BACL, 5-25 MM DTT, 3-4 % ISOPROPANOL, 10-15 MG/ML PROTEIN IN A 1:2 RATIO WITH THE RESERVOIR SOLUTION, HANGING DROP VAPOR DIFFUSION |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X26C / Wavelength: 1 |
Detector | Type: ADSC CCD / Detector: CCD / Details: A DOUBLY FOCUSING TOROIDAL MIRROR |
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 3.4→50 Å / Num. obs: 83695 / % possible obs: 93.9 % / Redundancy: 3.5 % / Rmerge(I) obs: 0.15 / Net I/σ(I): 7.8 |
Reflection shell | Resolution: 3.4→3.52 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 1.9 / % possible all: 69 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1JRO Resolution: 3.4→50 Å / Cor.coef. Fo:Fc: 0.898 / Cor.coef. Fo:Fc free: 0.841 / SU B: 64.606 / SU ML: 0.48 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R Free: 0.633 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES RESIDUAL ONLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 43.12 Å2
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Refinement step | Cycle: LAST / Resolution: 3.4→50 Å
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Refine LS restraints |
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